ABSTRACT There is a fundamental gap in our understanding of how host-parasite interactions maintain genetic variation within species, including humans. Interactions between humans and long-lived eukaryotic parasites may be the most important agents of natural selection across the human genome and may be responsible for the maintenance of genome-wide functional variation within humans (balancing selection). However, linking the agents of balancing selection with their genomic targets remains a major challenge. Continued existence of this gap is an important problem because until it is filled there is a limited understanding of the mechanisms responsible for potential maintenance of genetic variation within species. The long-term goal of the investigator's laboratory is to understand the genetic basis of host-parasite adaptations. The objective over the next five years is to identify agents and targets of selection arising from host-parasite interactions. The central hypothesis is that host-parasite interactions maintain genetic variation within species. The rationale is that transitions to parasitism on the genetic model plant Arabidopsis thaliana has occurred within the genetic model Drosophila lineage, allowing in-depth study. Guided by strong preliminary data, this hypothesis will be tested by pursuing these two overarching research questions: 1). Identify molecular genetic changes that underpin the transition to parasitism in a fly, 2) Determine if host-parasite interactions lead to the maintenance of genome-wide variation in flies and plants. Under the first question, the genomic architecture underlying the evolutionary transition to parasitism will be identified in the Drosophilidae. Next-generation sequencing and comparative genomics studies will identify genes necessary for the evolution parasitism from free living fruit flies. Preliminary studies show that this approach holds great promise for finding ?parasite-genes? and that the approach is feasible in the applicants' hands. Under the second question, populations of parasitic flies will be evolved with single or mixed host genotypes that vary in resistance traits. An evolve-and-resequence approach will test if genome-wide variation is maintained by balancing selection in flies. In the plants, a genome-wide association (GWAS) study approach will be used to identify loci associated with resistance to flies. The applicants have shown that these approaches will identify targets of balancing selection. Under both aims, functional studies using in vitro and in vivo approaches will be used to link evolutionary patterns with functional phenotypes. The proposed research is significant because it will be the first study in a continuum of research expected to lead to an integrative understanding of the role that host-parasite interactions play in shaping patterns of genome evolution. There is promise that general principles will be discovered relating to the role host-parasite interactions play in the maintenance of genetic variation. The research proposed is innovative because it represents a departure from current approaches to studies on the evolution of host-parasite interactions, which are restricted to microbes or non-model systems.